The benefits of commuting to Melbourne via rail are becoming harder to keep track of, a number of Bendigo line commuters say.

Faced with disruptions to timetables and increased commuting times, some are even ditching train travel altogether and switching to driving.

The commuters' frustrations come after the July opening of Regional Rail Link's new dedicated track for Bendigo and Ballarat lines and new timetable changes coming into effect from this week.

Bendigo line commuter Josh Meadows, who lives in Castlemaine but commutes to Melbourne three times a week, said the original morning express service oncemade his trip to work “viable and easy”.

Mr Meadows said recent changes such as earlier departure times, increased stations stops and slower trains meant the benefits of the Regional Rail Link were not clear.

He said the new rail link bypass also meant Bendigo commuters could no longer stop at North Melbourne station to connect with Melbourne's north.

"Four-and-a-half years ago the morning express got me from Castlemaine to North Melbourne in one hour. Now it takes an hour-and-a-half," he said.

“I can’t understand how, after all the years of track work and buses every school holidays, the Regional Rail Link has actually made our train trips to the city longer, not shorter.

“The state government should be concerned about this, as slower trains will not encourage more people to live in regional areas and commute to work in Melbourne.”

Castlemaine's Bernadette Ervin said she had been using the same service once a week for about four years, but started driving when the Regional Rail Link work began.

"There’s no real advantage for me catching the train anymore," she said.

"It's much easier for me to get in the car, even as one person - which I am philosophically opposed to - than deal with the stress of my train commute now.

"It used to be quite a convenient service but it’s not now. It’s maximum inconvenience for regional commuters."

She said having to change trains at Footscray rather than North Melbourne meant she had to "run like mad" to catch the next connecting train to get to work on time.

"What happens is you arrive at Footscray and you get spat out of the station and then have to get back in to the station," she said.

"Then you miss your connecting train and have to get the later train, so it’s about a 10 minute delay."

Woodvale resident Bruce Henderson, who works in Collingwood, has been jumping on the morning express service from Bendigo to Melbourne every day for six years.

But he said he was recently inspired to start driving after his two-hour door-to-door commute became almost three.

"I’m now going to drive down one day a week every week, just so I can gain three hours of my life back each week," he said.

A Public Transport Victoria spokesperson said the benefits of the Regional Rail Link would be fully realised when construction was complete in early 2015.

Bendigo trains began running on dedicated tracks between Sunshine and Southern Cross Station in mid-July.

"Passengers will continue to see changes, including extra services, as further stages of the project are complete," the spokesman said.

Regional Rail Link Authority spokesperson Bob Neilson said the project was a multi-billion investment in better train services for Bendigo.

He said removing North Melbourne was about removing one of the "biggest bottlenecks" in the metro system, which would increase reliability and capacity for both regional and metropolitan services.

"While this is a travel change for passengers, the benefit is that trains from Bendigo no longer get stuck behind Metro trains between Sunshine and the city, reducing unscheduled delays and creating space to run more Bendigo services in the future," he said.

Footscray station was in the process of being transformed into a modern transport interchange with capacity to manage thousands of metropolitan and regional customers daily, Mr Neilson said.

Construction of the project is on track to be complete this year, with services due to start running on along the entire alignment in the first half of 2015, he said.